Support the new strict option to fre catalog build

docs/tools/catalog.rst

@@ -1,19 +1,26 @@
 .. NEEDS UPDATING #TODO
 
-For more complete information on the ``catalogbuilder`` tool, please see its offical `documentation <https://noaa-gfdl.github.io/CatalogBuilder/>`_.
+For more complete information on the ``catalogbuilder`` tool, please see its official `documentation <https://noaa-gfdl.github.io/CatalogBuilder/>`_.
 
-``builder``
+``build``
 -----------
 
 Generate a catalog.
 
 * Builds json and csv format catalogs from user input directory path
-* Minimal Syntax: ``fre catalog builder -i [input path] -o [output path]``
+* Minimal Syntax: ``fre catalog build -i [input path] -o [output path]``
 * Module(s) needed: n/a
-* Example: ``fre catalog builder -i /archive/am5/am5/am5f3b1r0/c96L65_am5f3b1r0_pdclim1850F/gfdl.ncrc5-deploy-prod-openmp/pp -o ~/output --overwrite``
+* Example: ``fre catalog build -i /archive/am5/am5/am5f3b1r0/c96L65_am5f3b1r0_pdclim1850F/gfdl.ncrc5-deploy-prod-openmp/pp -o ~/output --overwrite``
 
 
 ``validate``
 ------------
 
-Validate the catalog.
+Validate a catalog
+
+* Runs the comprehensive validator tool (validates vocabulary and ensures catalogs were generated properly)
+* Minimal Syntax: ``fre catalog validate [json_path] --vocab     OR
+                    fre catalog validate [json_path] --proper_generation``
+* Module(s) needed: n/a
+* Example: ``fre catalog validate ~/example_catalog.json --vocab``
+

environment.yml

@@ -18,6 +18,7 @@ dependencies:
   - conda-forge::jsonschema
   - conda-forge::metomi-rose
   - conda-forge::nccmp
+  - conda-forge::numpy<2
   - conda-forge::pylint
   - conda-forge::pytest
   - conda-forge::pytest-cov

fre/catalog/frecatalog.py

@@ -4,9 +4,8 @@
 
 import click
 
-#import catalogbuilder
 from catalogbuilder.scripts import gen_intake_gfdl
-from catalogbuilder.scripts import test_catalog
+from catalogbuilder.tests import compval
 from catalogbuilder.scripts import combine_cats
 
 
@@ -32,23 +31,29 @@ def catalog_cli():
 @click.option('--append', is_flag = True, default = False)
 @click.option('--slow', is_flag = True, default = False,
     help = "Open NetCDF files to retrieve additional vocabulary (standard_name and intrafile static variables")
+@click.option('--strict', is_flag = True, default = False,
+    help = "Ensure output catalog is strictly compliant with schema")
 @click.pass_context
-def builder(context, input_path = None, output_path = None, config = None, filter_realm = None,
-            filter_freq = None, filter_chunk = None, verbose = False, overwrite = False, append = False, slow = False):
+def build(context, input_path = None, output_path = None, config = None, filter_realm = None,
+          filter_freq = None, filter_chunk = None, verbose = False, overwrite = False, append = False, slow = False, strict = False):
     # pylint: disable=unused-argument
     """ - Generate .csv and .json files for catalog """
     context.forward(gen_intake_gfdl.create_catalog_cli)
 
 @catalog_cli.command()
 @click.argument('json_path', nargs = 1 , required = True)
 @click.argument('json_template_path', nargs = 1 , required = False)
+@click.option('--vocab', is_flag=True, default = False,
+              help="Validates catalog vocabulary")
+@click.option('-pg','--proper_generation', is_flag=True, default = False,
+              help="Ensures that catalog has been 'properly generated' (No empty columns, reflects template)")
 @click.option('-tf', '--test-failure', is_flag=True, default = False,
               help="Errors are only printed. Program will not exit.")
 @click.pass_context
-def validate(context, json_path, json_template_path, test_failure):
+def validate(context, json_path, json_template_path, vocab, proper_generation, test_failure):
     # pylint: disable=unused-argument
-    """ - Validate a catalog against catalog schema """
-    context.forward(test_catalog.main)
+    """ - Validate catalogs against controlled vocabulary as provided by particular JSON schemas per vocabulary type (vocabulary validation) OR Validate a catalog against catalog schema template (proper generation checking) """
+    context.forward(compval.main)
 
 @catalog_cli.command()
 @click.option('--input', required = True, multiple = True,

fre/catalog/tests/test_fre_catalog.py

@@ -1,4 +1,4 @@
-
+'''This test ensures that the catalog builder module can be imported'''
 def test_fre_catalog_import():
     from fre import catalog
     assert catalog is not None

fre/tests/test_fre_catalog_cli.py

@@ -21,20 +21,14 @@ def test_cli_fre_catalog_opt_dne():
     result = runner.invoke(fre.fre, args=["catalog", "optionDNE"])
     assert result.exit_code == 2
 
-def test_cli_fre_catalog_builder():
-    ''' fre catalog builder '''
-    result = runner.invoke(fre.fre, args=["catalog", "builder"])
-    stdout_str = 'Missing: input_path or output_path. ' + \
-                 'Pass it in the config yaml or as command-line option'
-    assert all( [
-                  result.exit_code == 1,
-                  stdout_str in result.stdout.split('\n')
-                ]
-              )
-
-def test_cli_fre_catalog_builder_help():
-    ''' fre catalog builder --help '''
-    result = runner.invoke(fre.fre, args=["catalog", "builder", "--help"])
+def test_cli_fre_catalog_build():
+    ''' fre catalog build '''
+    result = runner.invoke(fre.fre, args=["catalog", "build"])
+    assert result.exit_code == 1
+
+def test_cli_fre_catalog_build_help():
+    ''' fre catalog build --help '''
+    result = runner.invoke(fre.fre, args=["catalog", "build", "--help"])
     assert result.exit_code == 0
 
 def test_cli_fre_catalog_merge():

meta.yaml

@@ -42,6 +42,7 @@ requirements:
     - conda-forge::jsonschema
     - conda-forge::metomi-rose
     - conda-forge::nccmp
+    - conda-forge::numpy<2
     - conda-forge::pylint
     - conda-forge::pytest
     - conda-forge::pytest-cov